At long last, my final PhD chapter is out: we developed a novel evolutionary simulator of bacterial pangenomes, Pansim, fitting it to data from >600K genomes using a likelihood-free framework, PopPUNK-mod, to explore neutral and adaptive pangenome dynamics www.biorxiv.org/content/10.6...
Aude Bernheim @audeber.bsky.social and Eugene Koonin discuss one of most interesting questions in the field connecting bacterial and animal immunity!
www.nature.com/articles/s41...
A new paper from the lab on virus-like particles called eCISs www.nature.com/articles/s41...
How bacteria evolved thousands of precision nanoinjectors?
Some bacteria don’t secrete toxins — they inject them using phage-derived machines called extracellular contractile injection systems (eCISs).
The Carney speech is worth reading in full: globalnews.ca/news/1162087...
Merry X-SMASH!
My first first author paper is out on bioRxiv! 🖥
We present epsSMASH, a comprehensive and high-throughput tool for predicting exopolysaccharide (exoPS) biosynthetic gene clusters (BGCs) in bacterial genomes 🦠🧬🧫
1/8
Thrilled to share our new review online with
@scottvedwards.bsky.social in @Trends Ecol & Evo! “pangenomics is rapidly transforming our ability to dissect the genetic basis of ecological and evolutionary change in natural systems.”
Test on Curtobacterium flaccumfaciens pv. flaccumfaciens genomes: www.ncbi.nlm.nih.gov/bioproject/P...
💾 Prokka 1.15.6 is released!
This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to.
#bioinformatics #microbiology #genomics
github.com/tseemann/pro...
Huge preprint if you are interested in bacterial strain taxonomy! The why and how of cgMLST LIN codes: An extensively revised and expanded version doi.org/10.1101/2024... I will summarize it for you in this thread 👇
Figure 1: (A) Anchor-based merging requires a common sequence (red) present in each partition. Multi-MUMs are merged by identifying overlaps between partition-specific matches in the anchor coordinate space, and a uniqueness threshold determines if a MUM is still unique in each partition after truncation. (B) String-based merging enables compu- tation of multi-MUMs between partitions without a common sequence. An example tree (left) is shown, highlighting the use case where partial multi-MUMs specific to internal nodes (starred) can be computed by merging subclade-based partitions up a tree. (right) MUM overlaps are computed by running Mumemto on the MUM sequences, and the uniqueness threshold array ensures overlaps remain unique across the merged dataset. (C) An example Burrows-Wheeler Transform (BWT), matrix (BWM), and Longest Com- mon Prefix (LCP) array, with sequence IDs for each suffix shown (ID). A non-maximal unique match (UM) is shown, and the uniqueness threshold for this match is found us- ing the flanking LCP values. (D) A partial multi-MUM (in blue) is found in all-but-one sequence (excluded in red). Using two anchor sequences (red and orange), all-but-one partial MUMs can be computed using an augmented anchor-based merging method (sec- tion 2.6).
Fantastic talk by @vikramshivakumar.bsky.social Mumemto—Scalable multi-MUM finding for pangenomes
Papers biorxiv.org/content/10.1101/2025.05.20.654611 & doi.org/10.1186/s13059-025-03644-0
Code: github.com/vikshiv/mume...
Very efficient pangenome visualization tool, revealing synteny and variations!
Hi everyone, a few years ago, we started a list of labs studying bacterial immunty for students, editors, conference organizers... (currently n=79).
Update time ! Send me a message to 1) add your lab or others 2) Correct info
docs.google.com/spreadsheets...
#Phagesky #Microsky
Do plasmids really move around that much? Well, maybe not always
Thrilled to have contributed to this story with two of my favourite microbiologists: @jrpenades.bsky.social & @sanmillan.bsky.social
This great work was led by Akshay Sabnis & @wfigueroac3.bsky.social
www.cell.com/cell-reports...
Movi 2: Fast and Space-Efficient Queries on Pangenomes. #Pangenomes #SequenceQueries #Genomics #Bioinformatics @biorxiv-genomic.bsky.social 🧬 🖥️
www.biorxiv.org/content/10.1...
Text reads “Antibiotic resistance is rising,” with an upward arrow and a “40%” warning icon. Below, a text box says: “Between 2018 and 2023, resistance increased in over 40% of the monitored pathogen–antibiotic combinations, with an annual rise of 5–15%.”
Between 2018–2023, antibiotic resistance increased in over 40% of the pathogen–antibiotic combinations monitored, with an average annual rise of 5–15%.
Resistance is highest in the WHO South-East Asian & Eastern Mediterranean Regions, where 1 in 3 reported infections were resistant 👉 bit.ly/438Ta1u
🧬 What if #plasmids weren’t competitors, but cooperators?
A new study in npj Antimicrobials & Resistance shows that many plasmids coexist within the same bacterium — and that non-resistant ones survive thanks to those carrying #AMR genes.
#AMR #Plasmids #OneHealth
🔗 doi.org/10.1038/s442...
Can we exploit past phage infection events (prophages) to decipher the specificity of phage receptor-binding proteins such as depolymerases?🔎 Happy to share our recent work at @natcomms.nature.com 🔽 #microsky #phagesky
www.nature.com/articles/s41...
#MicroSky
Sassy solves approximate string matching: finding all matches of a pattern in a text.
Sassy is out now!
Ever need to search for approximate matches of short DNA strings?
Sassy is the tool to use!
Available now wherever you get your code
With @rickbitloo.bsky.social
curiouscoding.nl/papers/sassy...
github.com/ragnarGrootK...
In this great new paper, the authors use metagenomic Hi-C to show that #phage with broad host range are fairly common, contrary to the prevailing view on their biology. Cutting edge methods like Hi-C are shedding light on our blind spots in the microbial world.
New pre-print from my lab!
Plasmids link antibiotic resistance and phage defense.
E.coli plasmids are hotspots for both antibiotic resistance and phage defense. Phage therapy has the potential to accidentally select for antibiotic resistance!!!
#microsky#AMR#phage
www.biorxiv.org/content/10.1....
Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n
Super paper from the mighty Mia Winkler, @genomarit.bsky.social and Iren Lohr.
"We have previously shown that there were relatively few strain-sharing events across ecological niches...plasmid-sharing is considerably more common across niches than strain-sharing. "
www.biorxiv.org/content/10.1...
CompareM2 is a genomes-to-report pipeline for comparing microbial genomes. #MicrobialGenomes #Bioinformatics 🧬 🖥️
academic.oup.com/bioinformati...
Identification and Functional Insights into New Phage Tail-Like Bacteriocins (PTLBs) Targeting Pseudomonas aeruginosa as new antimicrobials https://www.biorxiv.org/content/10.1101/2025.08.20.671207v1
Pangenome analysis of transposable element insertion polymorphisms reveals features underlying cold tolerance in rice. #TransposableElements #TE #Pangenomes #RiceGenomes @natcomms.nature.com
www.nature.com/articles/s41...
This is very cool. @sanmillan.bsky.social I wonder to what extend these non-random IS-dynamics are naturally selected for. Could it be the result of a long co-evolutionary history of ISs and bacteria? Are there differences in natural/non-natural antimicrobials?
www.biorxiv.org/content/10.1...
"We show that unrelated proteins have a universal tendency towards convergent evolution of secondary and tertiary motifs, causing an excess of high-scoring FP alignment... previous methods routinely overestimate significance by up to six orders of magnitude."
www.biorxiv.org/content/10.1...
Mumemto: efficient maximal matching across pangenomes. #Pangenomes #VisualizationTool #PangenomeDiagnostic #Bioinformatics #Genomics #GenomeBiology
genomebiology.biomedcentral.com/articles/10....
The first paper of my PhD is now available as a preprint! 🎉
Transposable elements (TEs) don't just jump within fungal genomes, they also move extensively between species. In this study, we screened over 1,300 fungal genomes and found a conservative estimate of 5,500+ horizontal transfer events.
Defence Systems are so hot right now 🔥 🔥 🔥 so check out our latest preprint to see how DSes contribute to niche adaptation, interact with each other, and drive accessory genome interactions in Pseudomonas aeruginosa 1/n
www.biorxiv.org/content/10.1...
